Splice Loss Research Articles

Abstract 4138407: Exome-wide association study of over a million individuals identified effector genes and variants for blood lipids

Background: Inherited hypercholesterolemia is an important Mendelian condition associated with early onset myocardial infarction. However, current genetic diagnostic criteria only partially explain severe clinical hypercholesterolemia. Furthermore, current pathogenicity categorizations do not consistently inform prognosis, but quantification is limited by scarcity of such rare variants. Aim: Exploiting populations scale genotype/phenotype data, to determine the architecture of the genetic variants associating with blood lipid levels with quantitative assessments. Methods: Here, we discovered and characterized rare coding alleles contributing to genetic dyslipidemia, a principal risk for coronary artery disease, among over a million individuals combining two large contemporary genetic datasets (Million Veteran Program N = 626,554 and UK Biobank, N = 431,026). Results: Testing 2,869,269 rare (minor allele frequency < 1%), coding variants, we identified 793 exome-wide significant associations ( P < 4.4 × 10 -11 ), including 8 previously undiscovered loci. Associated alleles are highly enriched in functional variant classes; high confidence predicted loss of function, deleterious missense, and cryptic splicing, showed significant and recessive associations, had similar effects across populations. Overall, rare variants contributed to additional > 16% of genetic trait variances on top of common genetic variants. The effect estimates of associated signals confirmed and refined curated pathogenic database, highlighted by the identification of African or South Asian specific pathogenic alleles previously controversial in its pathogenicity. Conclusion: This study provides resources and insights for understanding causal mechanisms and quantifying the expressivity of rare coding alleles for blood lipids by large scale sequencing study. Furthermore, identifying and characterizing population enriched variants, our study underscored the importance of multi-population rare variant study.

Estimation of splice losses between a photonic crystal fiber and a conventional single mode fiber and between two different photonic crystal fibers without and with transverse offset and angular misalignment

Estimation of splice losses between a photonic crystal fiber and a conventional single mode fiber and between two different photonic crystal fibers without and with transverse offset and angular misalignment

Splice Loss Investigation of Single-Mode Fiber and Photonic Crystal Fibers and Its Potential Refractometric Sensing Applications

Splice Loss Investigation of Single-Mode Fiber and Photonic Crystal Fibers and Its Potential Refractometric Sensing Applications

CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function.

Given the mounting evidence implicating TDP-43 dysfunction in several neurodegenerative diseases, there is a pressing need to establish accessible tools to sense and quantify TDP-43 loss-of-function (LOF). These tools are crucial for assessing potential disease contributors and exploring therapeutic candidates in TDP-43 proteinopathies. Here, we develop a sensitive and accurate real-time sensor for TDP-43 LOF: the CUTS (CFTR UNC13A TDP-43 Loss-of-Function) system. This system combines previously reported cryptic exons regulated by TDP-43 with a reporter, enabling the tracking of TDP-43 LOF through live microscopy and RNA/protein-based assays. We demonstrate CUTS' effectiveness in detecting LOF caused by TDP-43 mislocalization and RNA binding dysfunction, and pathological aggregation. Our results highlight the sensitivity and accuracy of the CUTS system in detecting and quantifying TDP-43 LOF, opening avenues to explore unknown TDP-43 interactions that regulate its function. In addition, by replacing the fluorescent tag in the CUTS system with the coding sequence for TDP-43, we show significant recovery of its function under TDP-43 LOF conditions, highlighting CUTS' potential for self-regulating gene therapy applications. In summary, CUTS represents a versatile platform for evaluating TDP-43 LOF in real-time and advancing gene-replacement therapies in neurodegenerative diseases associated with TDP-43 dysfunction.

Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion

TDP-43 protein is dysregulated in several neurodegenerative diseases, which often have a multifactorial nature and may have extrinsic stressors as a "second hit." TDP-43 undergoes reversible nuclear condensation in stressed cells including neurons. Here, we demonstrate that stress-inducible nuclear TDP-43 condensates are RNA-depleted, non-liquid assemblies distinct from the known nuclear bodies. Their formation requires TDP-43 oligomerization and ATP and is inhibited by RNA. Using a confocal nanoscanning assay, we find that amyotrophic lateral sclerosis (ALS)-linked mutations alter stress-induced TDP-43 condensation by changing its affinity to liquid-like ribonucleoprotein assemblies. Stress-induced nuclear condensation transiently inactivates TDP-43, leading to loss of interaction with its protein binding partners and loss of function in splicing. Splicing changes are especially prominent and persisting for STMN2 RNA, and STMN2 protein becomes rapidly depleted early during stress. Our results point to early pathological changes to TDP-43 in the nucleus and support therapeutic modulation of stress response in ALS.

Abstract 1201: Pervasive HLA disruption fuels cancer evolution

Abstract Disruption of the human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. However, although genomic loss of HLA is frequent in non-small cell lung cancer (NSCLC) and in some types of breast cancer, the extent and importance of transcriptomic disruption to HLA presentation, including transcript repression and alternative splicing (AS), remains unclear. To address this, we developed MHC Hammer, a tool to call HLA allele-specific mutations, loss of heterozygosity (LOH), transcriptional repression, and alternative splicing. We first assessed HLA allelic expression and the prevalence of AS in normal tissue. Applying MHC Hammer to 510 normal lung samples and 407 normal breast samples from the Genotype-Tissue Expression cohort, we identified extensive heterogeneity in HLA allelic expression depending on both the allele and tissue type. In addition, HLA allelic AS, occurring in at least 20% of the allele transcripts, was observed in 19% of normal lung and 13% of normal breast samples. Next, we applied MHC Hammer to 413 TRACERx NSCLCs and 743 TCGA breast tumours. While mutations were uncommon, HLA LOH was a frequent event, occurring in 32% of lung adenocarcinomas (LUAD) and 57% of lung squamous cell carcinomas (LUSC). We observed a similar rate of HLA LOH in estrogen receptor positive (ER+) and negative (ER-) tumors (ER+: 14%, ER-: 15%), while in triple negative breast tumours we observed a higher rate of LOH (31%). Due to the heterogeneity in HLA expression observed in the normal samples, to measure tumor specific HLA repression and alternative splicing, we restricted our analysis to tumours with WES, tumor and tumor-adjacent normal RNAseq data. This resulted in a cohort of 88 NSCLCs from the TRACERx study as well as 44 ER+ breast tumours from the TCGA cohort. 61% of LUAD, 75% of LUSC and 35% of ER+ tumours harbored class I HLA transcriptional repression that could not be explained by underlying genomic loss. 27% of LUAD, 7% of LUSC and 55% of ER+ breast tumor patients exhibited no HLA disruption. Tumor specific AS affecting HLA exons 2, 3 or 4, potentially disrupting HLA antigen presentation, was identified in 8% of LUADs, 11% of LUSC and 7% of ER+ breast tumours. Tumor specific AS of exon 5, yielding soluble HLA molecules without a transmembrane domain was identified in 20% of LUAD, 14% of LUSCs and 18% of ER+ breast tumours. LUAD and LUSC tumor regions without HLA LOH or repression were enriched for somatic HLA AS events and alleles with somatic HLA AS had a higher neoantigen burden than those without. We found no relationship between survival and HLA expression or AS in the normal tissue. However, consistent with the importance of HLA dysfunction in tumor evolution, LUADs with low HLA expression in at least one tumor region were associated with shorter disease-free survival, HLA LOH was more common in LUAD’s that metastasized and HLA repression was enriched in LUSC primary regions seeding metastases. Citation Format: Clare Puttick, Thomas P. Jones, Michelle Leung, Oriol Pich, Felipe Galvez Cancino, Jiali Liu, Manuel Varas-Godoy, Andrew Rowan, Carlos Martinez-Ruiz, Robert Bentham, Krijn K. Dijkstra, Rachel Rosenthal, Nnennaya Kanu, Kevin Litchfield, Roberto Salgado, David A. Moore, Peter Van Loo, Mariam Jamal-Hanjani, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton. Pervasive HLA disruption fuels cancer evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1201.

Differentiated Focal Plane Assisted Multi-core Fiber Fusion Splice Loss Evaluation

Differentiated Focal Plane Assisted Multi-core Fiber Fusion Splice Loss Evaluation

Development of a Handheld Optical Fusion Splicer with a Wing Sleeve Optical Connector

FTTH (Fibre to the Home) uses a fusion splice field-assembled optical connector. The fusion splice field-assembled optical connector is connected and assembled using a generic fibre fusion splicer. However, general purpose fusion splicers make the device difficult to operate in the installation field because the fusion splicer is too large and heavy to handle. As a result, the fibre optic splice often breaks during the optical connector assembly process. This makes it difficult to apply fusion-spliced optical connectors in the FTTH field. To solve this problem, this paper proposes a fusion splicer for FTTH that can perform fusion splicing using a wing-type sleeve optical connector. The proposed fusion splicer, with a connection module with a lifting/lowering function, is implemented to connect and protect the wing-type sleeve field-assembled optical connector. In addition, by eliminating the tube heater used as a connection protection method in the existing fusion splicer, the power module is reduced. The developed fusion splicer was evaluated for assembly reliability through splice loss measurements and a comparison of assembling time with the existing fusion splicer.

Multiomic sequencing of paired primary and metastatic small bowel carcinoids.

Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.

Antiresonant hollow-core fiber Bragg grating design.

Fiber Bragg gratings (FBGs) inscribed in hollow-core fibers hold a potential to revolutionize the field of gas photonics by enhancing the performance and versatility of hollow-core fiber-based matter cells. By effectively transforming these cells into cavities, FBGs can significantly extend the effective length of light-matter interactions. Traditional FBG inscription methods cannot be extended to hollow-core fibers, because light in the fundamental mode is predominantly confined to the hollow region where an index change cannot be induced. In this Letter, we propose a bi-thickness dual-ring hollow-core antiresonant fiber (DRHCF) design that achieves substantial overlap between the fundamental mode and cladding glass in a well-controlled manner, ensuring a strong FBG response with a minimal insertion loss. Through detailed numerical investigations, we demonstrate the feasibility of creating a high reflection FBG in the DRHCF using standard FBG inscription techniques. The proposed device is expected to have a length of <1 cm and the insertion loss of <0.3 dB, including splice loss.

Performance analysis of photonic crystal fiber structure based on different highly nonlinear materials

Generally, fiber with a large mode area is desired for fiber laser and beam delivery applications. But the use of these fiber types is restricted to linear optical applications due to the lower value of the nonlinear coefficient. This paper investigates a single material-based photonic crystal fiber (PCF) with improved optical characteristics, applicable for linear and nonlinear optics. The light propagation in the structure is explored by applying finite element solver-based COMSOL multiphysics software. Five nonlinear optical materials are utilized as background material to get the optimized material with high performance PCF. Using this PCF, the improved optical properties of PCF such as moderate effective mode area of 115.85 [Formula: see text], chromatic dispersion, confinement loss of 10[Formula: see text] dB/m, the nonlinear coefficient of 543W[Formula: see text]Km[Formula: see text], splicing loss of 2.013 dB, and numerical aperture are numerically analyzed. This single-mode PCF also shows the low bending loss for the bending radius of 7[Formula: see text]mm. The amended PCF structure is found to be suitable for high-power fiber laser, supercontinuum generation, wavelength conversion, and slow-light generation.

Aging Effects on Installed Submarine Optical Cables

Aging effects in submarine optical cables were evaluated with OTDR measurements along 24 years’ time span. Logarithmic trend curves indicate a Lifetime of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\sim $ </tex-math></inline-formula> 75 years before penalty reaches the threshold value of 0.005 dB/km. Penalties from splice losses were found to be twofold higher than those from fiber attenuation. Aging effects in warehouse stored spare cables were tenfold higher than in deployed cables.

General and Reliable Azimuthal Alignment Algorithm for Low Loss Multicore Fiber Fusion Splicing

Multicore fiber is a promising spatial division multiplexing technology to increase the transmission bandwidth of optical fiber links in any given available spatial cross section. To connect multicore fibers, similar to single-core fibers, fusion splicing is an indispensable tool. Since multicore fibers cannot be circularly symmetric, precise transverse and azimuthal alignment is crucial to minimize the insertion loss penalty that would originate from even small offsets in the core locations of the two fibers to be spliced together. In this paper, a novel azimuthal alignment algorithm for multicore fiber splicing is presented. Since it is based on side-view images, it can also determine the twist rates of both fibers to be spliced and take these twist rates into account when calculating the optimum azimuthal alignment angle at the very ends of the two fibers. In the case of fibers with markers, i.e., fibers that are not rotationally symmetric, the relative and absolute polarities of the two fiber ends are computed as well. We present the formulation of the azimuthal alignment algorithm and demonstrate its stability and versatility for a wide range of fibers with vastly different geometries, core numbers and twist rates, including an offset single-core fiber. In the case of 4-core fibers with markers, we achieve average splice losses of less than 0.03 dB regardless of the polarity, which is a substantial advantage in terms of real-world applicability in the field. For a twisted 7-core fiber, we demonstrate an accurate twist rate detection with standard deviation < 1.4/m (turns per meter).

Transposable elements and xenobiotic resistance.

Transposable elements or TEs are well known drivers of adaptive change in plants and animals but their role in insecticide resistance remains poorly documented. This review examines the potential role of transposons in resistance and identifies key areas where our understanding remains unclear. Despite well-known model systems such as upregulation of Drosophila Cyp6g1, many putative examples lack functional validation. The potential types of transposon-associated changes that could lead to resistance are reviewed, including changes in up-regulation, message stability, loss of function and alternative splicing. Where potential mechanisms appear absent from the resistance literature examples are drawn from other areas of biology. Finally, ways are suggested in which transgenic expression could be used to validate the biological significance of TE insertion. In the absence of such functional expression studies many examples of the association of TEs and resistance genes therefore remain as correlations.

Improvement in fusion performance between G652.D fiber and Ultra-low-loss fiber by controlling discharge current of fusion splicer

Due to factors such as external environment, splicing tools and differences in the fiber material itself, there are still many problems with the fusion performance of different kinds of optical fibers hybrid splicing. Up to now, the theoretical studies and experimental results reported on the loss and strength of fusion joint under harsh conditions have been too few and incomplete. Therefore, we have investigated the key issues to be solved in fiber fusion process, and firstly analyzed thermal characteristics in melt region, comprising fiber dopants diffusion effect and fiber core expansion, and then discussed the effects of fusion current and fusion time on fusion temperature, splice loss and fusion strength. Besides, a calibration method to improve discharge current of fusion splicer is proposed and splice loss model and fusion strength model for different types of optical fibers are established. Furthermore, fiber fusion-splicing experiments have been conducted under adverse circumstances, obtaining a large amount of experimental data. The simulation results are basically consistent with the theoretical analysis. Ultimately, the method has been directly applied to the field fiber fusion engineering with good results.

Choice of step and near step profiles from splice loss analysis of trapezoidal index single mode fibers leading to a proposal of a longitudinal displacement sensor

In this paper, an in-depth investigation is carried out on the effect of aspect ratio on splice loss between a pair of identical single mode trapezoidal index fibers in the presence of longitudinal and transverse misalignments. Splice loss is, interestingly, observed to get reduced, with the increase of aspect ratio and becomes minimum for unit aspect ratio for step profiles. Also, it is nearing minimum for near-step profiles. So, if there exists a little imperfection, say about ten percent, from step index profile, there will be no significant increase in the loss than that in step profile. This extended loss-tolerant feature in the step and near-step region revalidates the choice of the available step profile, technically used in communication. Thus, even for a digression in fabrication, system users should feel confident to use it. The physical significance of the results is justified from basic diffraction ideas. Finally, the entire study leads to a novel proposal of a longitudinal displacement sensor through simple and straight-forward empirical formulation to estimate the longitudinal misalignment from the knowledge of the splice loss of widely available step index fiber simply with air in the gap.

Multiomic sequencing of paired primary and metastatic small bowel carcinoids

Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.

Impact of multicore fiber (MCF) opticals, cross-talk, radiative leakage loss, splice loss and propagation configuration on the system transmission performance

MCF design strongly impacts the fiber optical properties, cross-talk and radiative leakage-loss contributing to increased transmission-loss. A systematic study is presented of the impact of MCF optical properties, cross-talk, transmission-loss and splice-loss on transmission system SNR. Different trench/ moat assisted core-designs having effective area of 80μm2 and 112μm2 are evaluated in 1x2 MCF design for different inter-core distance, with the impact of cross-talk, radiative leakage loss and propagation configuration (bidirectional (counterpropagating)/ copropagating) studied on transmission SNR. Sensitivity of any increased average splice-loss because of multiple cores on the SNR has also been calculated and reported. It is predicted that the maximum SNR for the case of copropagating and bidirectional propagation occurs at an inter-core distance of 48–50μm and 44μm respectively. Even though the absolute maximum SNR is higher for designs with larger effective area, the overall capacity at 80μm2 for copropagating transmission can be larger as it may accommodate 4 uncoupled cores compared to only 2 uncoupled cores for Aeff=112μm2. © 2022 Author(s)

Ultralow-loss fusion splicing between antiresonant hollow-core fibers and antireflection-coated single-mode fibers with low return loss.

The Fresnel reflection of a splice from the air-silica interface between a hollow-core fiber (HCF) and a solid-core conventional fiber will increase the splicing loss and also cause possible instability of transmission. Here, for the first time, we develop a novel approach to fusion splicing an antireflection-coated (AR-coated) conventional fiber and an antiresonant HCF, which was generally claimed to be impossible because of the heat-induced damage of the coating, and achieve state-of-the-art ultralow fusion splicing loss less than 0.3 dB and a low return loss less than -28 dB by optimizing the splicing procedures and parameters. Our new fusion splicing approach will benefit the wide application of HCFs in telecoms, laser technologies, gyroscopes, and fiber gas cells.

Transcript capture and ultradeep long-read RNA sequencing (CAPLRseq) to diagnose HNPCC/Lynch syndrome

PurposeWhereas most human genes encode multiple mRNA isoforms with distinct function, clinical workflows for assessing this heterogeneity are not readily available. This is a substantial shortcoming, considering that up to...